The 4L60 will not work with an LT1. You need a 4L60E. You also need the computer for an LT1. The year of the LT1 is important, because they are different from year to year.
The air pump is probably shot...the bags in the shocks leak, and the compressor rums continuously until it seizes. You can put a fill port with a Schrader valve so you can pump the bags up at any airing station, and let them down when not needed. When you cut the front springs, measure the distance between the rim and wheel opening and write it down before you cut them, and after. When you reassemble the front end, remove 1/32 inch shim from each stack for every 1/2 inch of drop to compensate for incurred negative camber. BTW, you can not cut the rear springs.
Just be careful when removing the door panel. Cut the tree fasteners with a sharp razor knife or razor in a scraper. You can get long knife blades with teeth as well. Your outside wipe is hardened, and probably clogged with grit, causing your glass to get scratched when you move the glass up and down.
I do not know what kind of wagon you have. If you have a vista window, the rear corners may be rusted, or the back of the rear support may be rusted through. It could be rusted anywhere around the perimeter of the window, or the sealant may be compromised.
Any leak along the quarter glass or body seam under the roof rack side runners will dump water in the top of the headliner, and it runs to the back, down the D pillar or the grab handles. That puts water in the tire well. Make sure the hole on the bottom of the spare well is open to drain the water out. I sealed the body seam by gouging out the old cracked sealant, and put roof sealer (house) in the groove. Do not put too much in the groove, or your roof rack will not fit properly.
You can check for leaks by putting a shop vac in the car with the hose sticking out of the wing window, and sealed with tape and cardboard. Then put bubble liquid (children's bubble liquid) on the seams. If it bubbles, you have found your leak. You should also seal the intake for the HVAC system before pressurizing the car for maximum effect.